Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa
  Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/4b/caf5a872ff459ccff6f0128ed4e488/.command.sh
  Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/90/f1d6080fa9eb9eece2cee0f5c7e792/three.sorted.bam.bai
  Downloading: s3://fsdx-algo-644019535899-us-west-2-an/aschultz/bf-gui-test/small_padded.bed
  Downloading: s3://fsdx-algo-644019535899-us-west-2-an/aschultz/bf-gui-test/small.bed
  Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa.fai
  Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/4b/caf5a872ff459ccff6f0128ed4e488/.command.run
  Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/90/f1d6080fa9eb9eece2cee0f5c7e792/three.sorted.bam
==> STAGING COMPLETE (8 inputs)

/usr/local/lib/python3.11/site-packages/numpy/_core/fromnumeric.py:54: FutureWarning: 'DataFrame.swapaxes' is deprecated and will be removed in a future version. Please use 'DataFrame.transpose' instead.
  return bound(*args, **kwds)
[W::hts_idx_load3] The index file is older than the data file: three.sorted.bam.bai
[W::sam_hrecs_update_hashes] PG line with multiple ID tags. The first encountered was preferred - ID:bwa-mem2
[mpileup] 1 samples in 1 input files
[mpileup] Combined max depth is above 1M. Potential memory hog!
[W::hts_idx_load3] The index file is older than the data file: three.sorted.bam.bai
[W::sam_hrecs_update_hashes] PG line with multiple ID tags. The first encountered was preferred - ID:bwa-mem2
[mpileup] 1 samples in 1 input files
[mpileup] Combined max depth is above 1M. Potential memory hog!
[W::hts_idx_load3] The index file is older than the data file: three.sorted.bam.bai
[W::sam_hrecs_update_hashes] PG line with multiple ID tags. The first encountered was preferred - ID:bwa-mem2
[mpileup] 1 samples in 1 input files
[mpileup] Combined max depth is above 1M. Potential memory hog!
[W::hts_idx_load3] The index file is older than the data file: three.sorted.bam.bai
[W::sam_hrecs_update_hashes] PG line with multiple ID tags. The first encountered was preferred - ID:bwa-mem2
[mpileup] 1 samples in 1 input files
[mpileup] Combined max depth is above 1M. Potential memory hog!
[W::hts_idx_load3] The index file is older than the data file: three.sorted.bam.bai
[W::sam_hrecs_update_hashes] PG line with multiple ID tags. The first encountered was preferred - ID:bwa-mem2
[mpileup] 1 samples in 1 input files
[mpileup] Combined max depth is above 1M. Potential memory hog!
[W::hts_idx_load3] The index file is older than the data file: three.sorted.bam.bai
[W::sam_hrecs_update_hashes] PG line with multiple ID tags. The first encountered was preferred - ID:bwa-mem2
[mpileup] 1 samples in 1 input files
[mpileup] Combined max depth is above 1M. Potential memory hog!
[W::hts_idx_load3] The index file is older than the data file: three.sorted.bam.bai
[W::sam_hrecs_update_hashes] PG line with multiple ID tags. The first encountered was preferred - ID:bwa-mem2
[mpileup] 1 samples in 1 input files
[mpileup] Combined max depth is above 1M. Potential memory hog!
[W::hts_idx_load3] The index file is older than the data file: three.sorted.bam.bai
[W::sam_hrecs_update_hashes] PG line with multiple ID tags. The first encountered was preferred - ID:bwa-mem2
[mpileup] 1 samples in 1 input files
[mpileup] Combined max depth is above 1M. Potential memory hog!
[W::hts_idx_load3] The index file is older than the data file: three.sorted.bam.bai
[W::sam_hrecs_update_hashes] PG line with multiple ID tags. The first encountered was preferred - ID:bwa-mem2
[mpileup] 1 samples in 1 input files
[mpileup] Combined max depth is above 1M. Potential memory hog!
[W::hts_idx_load3] The index file is older than the data file: three.sorted.bam.bai
[W::sam_hrecs_update_hashes] PG line with multiple ID tags. The first encountered was preferred - ID:bwa-mem2
[mpileup] 1 samples in 1 input files
[mpileup] Combined max depth is above 1M. Potential memory hog!
Done. Merging outputs